Gel versus capillary electrophoresis genotyping for categorizing treatment outcomes in two anti-malarial trials in Uganda

Table 1 Characteristics of genotyping msp2 using agarose gel versus capillary electrophoresis.

Study Location	Characteristic	Gel^a	CE^b	P value^c
Kanungu (n = 90)	Probability two randomly selected alleles will match by chance^d	0.066	0.025	<0.001
	MOI Day 0^e, mean (SD)	2.73 (1.53)	3.82 (2.58)	<0.001
	MOI Day F^f, mean (SD)	1.23 (1.14)	2.02 (1.82)	<0.001
	P_match ^g, median (IQR)	0.20 (0.11 - 0.36)	0.16 (0.06 - 0.26)	0.001
Apac (n = 209)	Probability two randomly selected alleles will match	0.061	0.028	<0.001
	MOI Day 0, mean (SD)	3.65 (1.80)	5.06 (3.42)	<0.001
	MOI Day F, mean (SD)	2.42 (1.59)	3.26 (2.62)	<0.001
	P_match, median (IQR)	0.41 (0.23 - 0.59)	0.27 (0.12 - 0.50)	<0.001

^a Gel, Agarose gel electrophoresis
^b CE, Capillary electrophoresis
^c P values testing the hypothesis Gel is different than CE using a bootstrap test for the probability two alleles will match by chance, and the Wilcoxon Rank Sum test for other characteristics
^d Calculated using the empiric distribution of Day 0 alleles and criteria for a match based on the electrophoresis method
^e Multiplicity of infection (number of alleles detected) on Day 0 (day of anti-malarial treatment)
^f Multiplicity of infection on Day F (day of failure, i.e. recurrent parasitaemia)
^g Probability of a genotyping match occurring by chance for each sample, calculated using the actual alleles present on Day 0 and the multiplicity of infection on Day F (MOI-F). Ten thousand random combinations of MOI-F alleles were chosen for Day F using the empiric frequency distribution, and P_match is the proportion of these combinations that had at least one allele match with the Day 0 alleles.

ISSN: 1475-2875